Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.
Male-sterility has been successfully used for enhancing yield in a number of cereal and vegetable crops. In food legumes, this technology could never be used either due to non-availability of natural outcrossing system, or an efficient male-sterility system or both. Pigeonpea [Cajanus cajan (L.) Millsp.] is a partially cross-pollinated food legume and recent success in breeding a stable male-sterility system has allowed breeders to exploit hybrid vigour for increasing yields. The cytoplasmic-nuclear male-sterility (CMS)-based hybrids have recorded 28.4% yield superiority over local checks in farmersÕ fields. This paper besides summarizing the reports of all the genetic and CMS systems, also discusses the prospects of utilizing these male-sterility systems in commercial hybrid breeding programmes.
Single nucleotide polymorphisms (SNPs) are ideal molecular markers due to their higher abundance. Although several types of genotyping platforms for assaying large number of SNPs are available, in cases such as marker-assisted selection, where few markers are required for genotyping a set of potential lines, highthroughput SNP genotyping platforms (e.g., iScan or Infinium) may not be cost effective. In this scenario, GoldenGate assays based on VeraCode technology using Illumina BeadXpress seems to be the most cost-effective platform. The objective of this study was to develop cost-effective SNP genotyping platforms in chickpea (Cicer arietinum L.) and pigeonpea (Cajanus cajan L.). Two sets of SNPs, one each for chickpea (96 SNPs) and pigeonpea (48 SNPs), were developed and tested by genotyping 288 diverse genotypes from respective reference sets. The SNPs selected for the oligo pool assays had high transferability to crop wild relative species. The mean polymorphism information content value of assayed SNP markers was 0.31 and 0.32 in chickpea and pigeonpea, respectively. No unique pattern was observed in the chickpea reference set whereas two major groups were observed in the case of the pigeonpea reference set. The Illumina BeadXpress platform assays developed for chickpea and pigeonpea are highly informative and cost effective for undertaking genetic studies in these legume species.
ICRISAT scientists, working with Indian programme counterparts, developed the world's first cytoplasmic-nuclear male sterility (CMS)-based commercial hybrid in a food legume, the pigeonpea [Cajanus cajan (L.) Millsp.]. The CMS, in combination with natural outcrossing of the crop, was used to develop viable hybrid breeding technology. Hybrid ICPH 2671 recorded 47% superiority for grain yield over the control variety 'Maruti' in multilocation on-station testing for 4 years. In the on-farm trials conducted in five Indian states, mean yield of this hybrid (1396 kg/ ha) was 46.5% greater than that of the popular cv. 'Maruti' (953 kg/ha). Hybrid ICPH 2671 also exhibited high levels of resistance to Fusarium wilt and sterility mosaic diseases. The outstanding performance of this hybrid has led to its release for cultivation in India by both a private seed company (as 'Pushkal') and a public sector university (as 'RV ICPH 2671'). Recent developments in hybrid breeding technology and high yield advantages realized in farmers' fields have given hope for a breakthrough in pigeonpea productivity.
To break the decades-old yield barrier in pigeonpea [Cajanus cajan (L.) Millsp.] a hybrid breeding technology was successfully developed and the first two hybrids were recently released in India. In order to produce heterotic hybrid combinations, the first logical step is the identification and selection of genetically diverse parents with favorable alleles. In this context, the concept of classifying hybrid parents into different heterotic groups was developed and successfully used in maize and later adopted in other crops. Since hybrid technology in pigeonpea is new, the authors have made the first attempt to identify heterotic groups using SCA effects of 102 crosses generated from line 9 tester mating and evaluated them at four locations. Based on the performance of hybrids in terms of SCA effects, seven heterotic groups were constituted. Besides this, a scheme to use this information in breeding high yielding hybrids with specific or wide adaptation is also discussed herein. Genetic diversity between lines and tester showed positive association with the heterotic pools generated on the basis of SCA.
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